Variant report

Variant	rs4364202
Chromosome Location	chr3:49151001-49151002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49141627..49143608-chr3:49150216..49151826,2	K562	blood:
2	chr3:49149941..49155379-chr3:49168130..49172281,5	MCF-7	breast:
3	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
4	chr3:49141404..49143688-chr3:49149848..49152173,2	K562	blood:
5	chr3:49131855..49133728-chr3:49150296..49151812,2	K562	blood:
6	chr3:49066078..49068307-chr3:49150098..49151644,2	MCF-7	breast:
7	chr3:49150618..49152436-chr3:49164299..49167178,2	K562	blood:
8	chr3:49055358..49059110-chr3:49149011..49151698,3	K562	blood:
9	chr3:49148001..49150538-chr3:49150834..49154953,4	K562	blood:
10	chr3:49144707..49154191-chr3:49155059..49160099,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000172046	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10154895	0.83[ASN][1000 genomes]
rs11552724	0.93[ASN][1000 genomes]
rs11706052	0.80[ASN][1000 genomes]
rs11706189	0.83[ASN][1000 genomes]
rs11712006	0.93[ASN][1000 genomes]
rs11713297	0.83[ASN][1000 genomes]
rs12487580	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12491743	0.84[AMR][1000 genomes]
rs12493001	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12636030	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12637037	0.83[ASN][1000 genomes]
rs13064784	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13072554	0.80[ASN][1000 genomes]
rs13080725	0.80[ASN][1000 genomes]
rs13316620	0.81[AFR][1000 genomes]
rs3212	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34326553	0.93[ASN][1000 genomes]
rs34580506	0.93[ASN][1000 genomes]
rs34889065	0.93[ASN][1000 genomes]
rs35108630	0.80[ASN][1000 genomes]
rs35283189	0.93[ASN][1000 genomes]
rs35673421	0.93[ASN][1000 genomes]
rs36133651	0.90[EUR][1000 genomes]
rs3923475	0.80[ASN][1000 genomes]
rs4072859	0.81[AFR][1000 genomes]
rs4279134	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4292260	0.83[AFR][1000 genomes]
rs4499638	0.80[ASN][1000 genomes]
rs4513485	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4521268	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4536858	0.80[ASN][1000 genomes]
rs4955410	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4955411	0.82[AFR][1000 genomes]
rs4955418	0.80[ASN][1000 genomes]
rs5030795	0.93[ASN][1000 genomes]
rs55713230	0.80[ASN][1000 genomes]
rs61583136	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62262517	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6770112	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6779394	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784111	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6789285	0.87[AMR][1000 genomes]
rs6790914	0.80[ASN][1000 genomes]
rs6795025	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7373790	0.86[AMR][1000 genomes]
rs7432989	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7615235	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7626445	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632267	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7645551	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9683094	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9835439	0.83[ASN][1000 genomes]
rs9837237	0.85[ASN][1000 genomes]
rs9837625	0.85[ASN][1000 genomes]
rs9840050	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9846123	0.85[AMR][1000 genomes]
rs9855123	0.83[ASN][1000 genomes]
rs9862483	0.83[ASN][1000 genomes]
rs9880088	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:23)

SNP	Gene	Cis/trans	Tissue	Source
rs4364202	WDR6	cis	Stomach	GTEx
rs4364202	CCDC36	cis	Esophagus Muscularis	GTEx
rs4364202	WDR6	cis	Muscle Skeletal	GTEx
rs4364202	CCDC36	cis	Artery Tibial	GTEx
rs4364202	WDR6	cis	Nerve Tibial	GTEx
rs4364202	AMT	cis	Muscle Skeletal	GTEx
rs4364202	NICN1-AS1	cis	Thyroid	GTEx
rs4364202	WDR6	cis	lung	GTEx
rs4364202	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4364202	WDR6	cis	Whole Blood	GTEx
rs4364202	AMT	cis	Whole Blood	GTEx
rs4364202	WDR6	cis	Esophagus Mucosa	GTEx
rs4364202	AMT	cis	Thyroid	GTEx
rs4364202	NCKIPSD	cis	Whole Blood	GTEx
rs4364202	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs4364202	WDR6	cis	Esophagus Muscularis	GTEx
rs4364202	NCKIPSD	cis	Nerve Tibial	GTEx
rs4364202	WDR6	cis	Heart Left Ventricle	GTEx
rs4364202	WDR6	cis	Adipose Subcutaneous	GTEx
rs4364202	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4364202	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4364202	NICN1	cis	Thyroid	GTEx
rs4364202	WDR6	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49142800-49156400	Weak transcription	Right Atrium	heart
2	chr3:49142800-49157200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:49142800-49157600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49143000-49153800	Weak transcription	Fetal Brain Male	brain
5	chr3:49143600-49155200	Strong transcription	Brain Cingulate Gyrus	brain
6	chr3:49143600-49156200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:49143600-49156200	Strong transcription	Brain Anterior Caudate	brain
8	chr3:49143600-49156200	Strong transcription	NHLF	lung
9	chr3:49143600-49156400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:49143600-49156400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:49143600-49156400	Strong transcription	Placenta	Placenta
12	chr3:49143600-49156400	Strong transcription	Fetal Stomach	stomach
13	chr3:49143600-49156400	Strong transcription	NHEK	skin
14	chr3:49143600-49156600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:49143600-49156600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:49143600-49156600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:49143600-49156600	Strong transcription	Fetal Thymus	thymus
18	chr3:49143600-49156800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:49143800-49155000	Strong transcription	Adipose Nuclei	Adipose
20	chr3:49143800-49155600	Strong transcription	Esophagus	oesophagus
21	chr3:49143800-49155800	Strong transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:49143800-49156200	Strong transcription	Liver	Liver
23	chr3:49143800-49156200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:49143800-49156400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:49143800-49156600	Strong transcription	Fetal Muscle Leg	muscle
26	chr3:49143800-49156600	Strong transcription	Osteobl	bone
27	chr3:49144000-49153000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:49144000-49155000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr3:49144000-49155600	Strong transcription	Brain Angular Gyrus	brain
30	chr3:49144000-49156200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:49144000-49156200	Strong transcription	Brain Germinal Matrix	brain
32	chr3:49144000-49156400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:49144000-49156800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:49144200-49156400	Strong transcription	Gastric	stomach
35	chr3:49144200-49156400	Strong transcription	Lung	lung
36	chr3:49144200-49156800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:49144600-49154000	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:49144600-49155200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:49144600-49155800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr3:49144600-49156400	Strong transcription	Fetal Brain Female	brain
41	chr3:49144600-49156400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:49144600-49156600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:49144600-49156600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:49144800-49155000	Strong transcription	Colon Smooth Muscle	Colon
45	chr3:49144800-49155000	Strong transcription	Right Ventricle	heart
46	chr3:49144800-49155600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:49144800-49155600	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr3:49144800-49155800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr3:49144800-49156000	Strong transcription	Aorta	Aorta
50	chr3:49144800-49156200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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